This project contains a template for molecular dynamics project, most commonly in NAMD.
The configuration of the project is hierachical.
The project basic configuration in the pro project root, namely files environment.tcl, runner.tcl and force field parameters. The environment file contains a basic setup for the simulation environment. The runner file performs the simulations based on the phase in effect.
Second level is the simulations. They contain a simulation specific configuration in file namd.tcl.
Third level is the individual runs. An example contain basic phases: minimization, warm, equilibration and production run. Their specific configuration is in the run configuration fiels, such as 00_minimize.namd.
Copy the project directory and modify to your specific needs. The configuration files are designed to be run from the run directories, e.g.
cd project/simulation/00_minimize
namd2 00_minimize.namd > 00_minimize.output 2> 00_minimize.error